#include <obopsimodterm.h>

Public Member Functions
	OboPsiModTerm ()

	~OboPsiModTerm ()

	OboPsiModTerm (const OboPsiModTerm &)

OboPsiModTerm &	operator= (const OboPsiModTerm &)

bool	isValid () const

bool	isA (const QString &accession) const
	tells if this term "is_a" another accession

void	setAccession (const QString &accession)

const QString &	getAccession () const

bool	isUnimod () const

Public Attributes
QString	m_name

QString	m_definition

QString	m_psiModLabel

QString	m_psiMsLabel

QString	m_diffFormula

QString	m_formula

QString	m_origin

double	m_diffMono

double	m_massMono

QStringList	m_isA

Private Member Functions
void	parseLine (const QString &line)

void	clearTerm ()

Private Attributes
friend	OboPsiMod

friend	OboPsiMs

friend	OboUnimod

QString	m_accession

bool	m_isUnimod = false

Static Private Attributes
static QRegularExpression	m_firstParse

static QRegularExpression	m_findExactPsiModLabel

static QRegularExpression	m_findRelatedPsiMsLabel

static QRegularExpression	m_firstParseUnimod

static QRegularExpression	m_parseDefinition

Detailed Description

Definition at line 33 of file obopsimodterm.h.

Constructor & Destructor Documentation

◆ OboPsiModTerm() [1/2]

pappso::OboPsiModTerm::OboPsiModTerm ( )

Definition at line 51 of file obopsimodterm.cpp.

52{

53}

Referenced by OboPsiModTerm(), and operator=().

◆ ~OboPsiModTerm()

pappso::OboPsiModTerm::~OboPsiModTerm ( )

Definition at line 55 of file obopsimodterm.cpp.

56{

57}

◆ OboPsiModTerm() [2/2]

pappso::OboPsiModTerm::OboPsiModTerm ( const OboPsiModTerm & other )

Definition at line 58 of file obopsimodterm.cpp.

{
  m_accession   = other.m_accession;
  m_name        = other.m_name;
  m_definition  = other.m_definition;
  m_psiModLabel = other.m_psiModLabel;
  m_psiMsLabel  = other.m_psiMsLabel;
  m_diffFormula = other.m_diffFormula;
  m_formula     = other.m_formula;
  m_origin      = other.m_origin;
 
  m_diffMono = other.m_diffMono;
  m_massMono = other.m_massMono;
  m_isA      = other.m_isA;
  m_isUnimod = other.m_isUnimod;
}

References OboPsiModTerm(), m_accession, m_definition, m_diffFormula, m_diffMono, m_formula, m_isA, m_isUnimod, m_massMono, m_name, m_origin, m_psiModLabel, and m_psiMsLabel.

Member Function Documentation

◆ clearTerm()

void pappso::OboPsiModTerm::clearTerm ( )

private

Definition at line 243 of file obopsimodterm.cpp.

{
  m_accession   = "";
  m_name        = "";
  m_definition  = "";
  m_psiModLabel = "";
  m_diffFormula = "";
  m_formula     = "";
  m_diffMono    = 0;
  m_origin      = "";
  m_massMono    = 0;
  m_isA.clear();
  m_isUnimod = false;
}

References m_accession, m_definition, m_diffFormula, m_diffMono, m_formula, m_isA, m_isUnimod, m_massMono, m_name, m_origin, and m_psiModLabel.

◆ getAccession()

const QString & pappso::OboPsiModTerm::getAccession ( ) const

Definition at line 261 of file obopsimodterm.cpp.

{
  return m_accession;
}

References m_accession.

Referenced by pappso::AaModification::createInstance(), pappso::OboTermForm::displayOboTerm(), pappso::AaModification::getInstance(), pappso::OboListWidget::onSelectionChanged(), pappso::ChemicalFormula::setOboPsiModTerm(), pappso::FilterOboPsiModMap::setOboPsiModTerm(), pappso::FilterOboPsiModTermAccession::setOboPsiModTerm(), and pappso::MzIdentMlWriter::writeCvParam().

◆ isA()

bool pappso::OboPsiModTerm::isA ( const QString & accession ) const

tells if this term "is_a" another accession

Returns: bool if true

Definition at line 102 of file obopsimodterm.cpp.

{
  return m_isA.contains(accession);
}

References m_isA.

Referenced by pappso::ChemicalFormula::setOboPsiModTerm().

◆ isUnimod()

bool pappso::OboPsiModTerm::isUnimod ( ) const

Definition at line 277 of file obopsimodterm.cpp.

{
  return m_isUnimod;
}

References m_isUnimod.

Referenced by pappso::ChemicalFormula::setOboPsiModTerm().

◆ isValid()

bool pappso::OboPsiModTerm::isValid ( ) const

Definition at line 96 of file obopsimodterm.cpp.

{
  return (!m_accession.isEmpty());
}

References m_accession.

Referenced by pappso::OboTermForm::displayOboTerm().

◆ operator=()

OboPsiModTerm & pappso::OboPsiModTerm::operator= ( const OboPsiModTerm & other )

Definition at line 76 of file obopsimodterm.cpp.

{
  m_accession   = other.m_accession;
  m_name        = other.m_name;
  m_definition  = other.m_definition;
  m_psiModLabel = other.m_psiModLabel;
  m_psiMsLabel  = other.m_psiMsLabel;
  m_diffFormula = other.m_diffFormula;
  m_formula     = other.m_formula;
  m_origin      = other.m_origin;
 
  m_diffMono = other.m_diffMono;
  m_massMono = other.m_massMono;
  m_isA      = other.m_isA;
  m_isUnimod = other.m_isUnimod;
  return *this;
}

References OboPsiModTerm(), m_accession, m_definition, m_diffFormula, m_diffMono, m_formula, m_isA, m_isUnimod, m_massMono, m_name, m_origin, m_psiModLabel, and m_psiMsLabel.

◆ parseLine()

void pappso::OboPsiModTerm::parseLine ( const QString & line )

private

Definition at line 108 of file obopsimodterm.cpp.

{
  // qDebug() << "OboPsiModTerm::parseLine begin " << line;
  //  id: MOD:00007
  //  is_a: MOD:01441 ! natural, standard, encoded residue
  QRegularExpressionMatch match_line = m_firstParse.match(line);
  if(match_line.hasMatch())
    {
      QStringList pline = match_line.capturedTexts();
      // qDebug() << "OboPsiModTerm::parseLine match " << pline[0] << pline[1];
      if(pline[1] == "id")
        {
          setAccession(pline[2].trimmed());
          // qDebug() << "OboPsiModTerm::parseLine accession = " << m_accession;
        }
      else if(pline[1] == "name")
        {
          m_name = pline[2].trimmed();
          // qDebug() << "OboPsiModTerm::parseLine accession = " << m_accession;
        }
      else if(pline[1] == "is_a")
        {
          m_isA << pline[2].section(" ", 0, 0);
          // qDebug() << "OboPsiModTerm::parseLine is_a = " << m_isA.join(" ");
        }
      else if(pline[1] == "xref")
        {
 
          // xref: DiffMono: "1.007276"
          QRegularExpressionMatch match_subline = m_firstParse.match(pline[2]);
          if(m_isUnimod)
            {
              match_subline = m_firstParseUnimod.match(pline[2]);
            }
          if(match_subline.hasMatch())
            {
              QStringList psecond = match_subline.capturedTexts();
              if(psecond[1] == "DiffMono")
                {
                  m_diffMono = psecond[2].replace("\"", "").toDouble();
                  // qDebug() << "OboPsiModTerm::parseLine m_diffMono = " <<
                  // m_diffMono;
                }
              else if(psecond[1] == "delta_mono_mass")
                { // UNIMOD
                  // xref: delta_mono_mass "42.010565"
                  m_diffMono = psecond[2].replace("\"", "").toDouble();
                  // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" <<
                  // m_diffFormula<<"|";
                }
              else if(psecond[1] == "DiffFormula")
                {
                  m_diffFormula = psecond[2].trimmed().replace("\"", "");
                  // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" <<
                  // m_diffFormula<<"|";
                }
 
              else if(psecond[1] == "delta_composition")
                {
                  // UNIMOD
                  // xref: delta_composition "H(2) C(2) O"
                  m_diffFormula = psecond[2].trimmed().replace("\"", "");
                  // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" <<
                  // m_diffFormula<<"|";
                }
 
              else if(psecond[1] == "Formula")
                {
                  // xref: Formula: "C 5 H 9 N 1 O 1 S 1"
                  m_formula = psecond[2].trimmed().replace("\"", "");
                  // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" <<
                  // m_diffFormula<<"|";
                }
              else if(psecond[1] == "Origin")
                {
                  m_origin = psecond[2].trimmed().replace("\"", "").replace(",", "");
                  // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" <<
                  // m_diffFormula<<"|";
                }
              // xref: MassMono: "71.037114"
 
              else if(psecond[1] == "MassMono")
                {
                  bool is_ok       = false;
                  double mass_mono = psecond[2].replace("\"", "").toDouble(&is_ok);
                  if(is_ok)
                    m_massMono = mass_mono;
                  else
                    m_massMono = 0;
                  // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" <<
                  // m_diffFormula<<"|";
                }
            }
        }
      else if(pline[1] == "synonym")
        {
          // synonym: "Se(S)Res" EXACT PSI-MOD-label []
          QRegularExpressionMatch match_exact_psimod = m_findExactPsiModLabel.match(pline[2]);
          if(match_exact_psimod.hasMatch())
            {
              m_psiModLabel = match_exact_psimod.captured(1).trimmed().replace("\"", "");
              // qDebug() << "OboPsiModTerm::parseLine m_psiModLabel = |" <<
              // m_psiModLabel<<"|";
            }
          else
            {
              QRegularExpressionMatch match_related_psims = m_findRelatedPsiMsLabel.match(pline[2]);
              if(match_related_psims.hasMatch())
                {
                  m_psiMsLabel = match_related_psims.captured(1).trimmed().replace("\"", "");
                  // qDebug() << "OboPsiModTerm::parseLine m_psiModLabel = |" <<
                  // m_psiModLabel<<"|";
                }
            }
        }
      else if(pline[1] == "def")
        {
          // def: "A protein modification that modifies an L-asparagine
          // residue." [PubMed:18688235]
 
          QRegularExpressionMatch match_subline = m_parseDefinition.match(pline[2]);
 
          if(match_subline.hasMatch())
            {
              QStringList psecond = match_subline.capturedTexts();
              m_definition        = psecond[1];
            }
          else
            {
              m_definition = pline[2];
            }
        }
    }
}

References line, m_definition, m_diffFormula, m_diffMono, m_findExactPsiModLabel, m_findRelatedPsiMsLabel, m_firstParse, m_firstParseUnimod, m_formula, m_isA, m_isUnimod, m_massMono, m_name, m_origin, m_parseDefinition, m_psiModLabel, m_psiMsLabel, and setAccession().

◆ setAccession()

void pappso::OboPsiModTerm::setAccession ( const QString & accession )

Definition at line 267 of file obopsimodterm.cpp.

{
  qDebug() << accession;
  m_isUnimod  = false;
  m_accession = accession;
  if(m_accession.startsWith("UNIMOD:"))
    m_isUnimod = true;
}

References m_accession, and m_isUnimod.

Referenced by pappso::AaModification::createInstance(), pappso::AaModification::createInstanceC13N15LabelledAminoAcid(), pappso::MsFileAccessor::getOboPsiModTermFileFormat(), pappso::PwizMsRunReader::getOboPsiModTermNativeIDFormat(), and parseLine().

Member Data Documentation

◆ m_accession

QString pappso::OboPsiModTerm::m_accession

private

Definition at line 82 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), getAccession(), isValid(), operator=(), and setAccession().

◆ m_definition

QString pappso::OboPsiModTerm::m_definition

Definition at line 59 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), pappso::OboTermForm::displayOboTerm(), pappso::MsFileAccessor::getOboPsiModTermFileFormat(), pappso::PwizMsRunReader::getOboPsiModTermNativeIDFormat(), operator=(), and parseLine().

◆ m_diffFormula

QString pappso::OboPsiModTerm::m_diffFormula

Definition at line 62 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), pappso::AaModification::createInstance(), pappso::AaModification::createInstanceC13N15LabelledAminoAcid(), pappso::OboTermForm::displayOboTerm(), operator=(), parseLine(), and pappso::ChemicalFormula::setOboPsiModTerm().

◆ m_diffMono

double pappso::OboPsiModTerm::m_diffMono

Definition at line 66 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), pappso::AaModification::createInstance(), pappso::AaModification::createInstance(), pappso::AaModification::createInstanceC13N15LabelledAminoAcid(), pappso::OboTermForm::displayOboTerm(), pappso::OboListProxyModel::filterAcceptsRow(), pappso::OboListProxyModel::lessThan(), operator=(), parseLine(), and pappso::FilterOboPsiModTermDiffMono::setOboPsiModTerm().

◆ m_findExactPsiModLabel

QRegularExpression pappso::OboPsiModTerm::m_findExactPsiModLabel

staticprivate

Definition at line 76 of file obopsimodterm.h.

Referenced by parseLine().

◆ m_findRelatedPsiMsLabel

QRegularExpression pappso::OboPsiModTerm::m_findRelatedPsiMsLabel

staticprivate

Definition at line 77 of file obopsimodterm.h.

Referenced by parseLine().

◆ m_firstParse

QRegularExpression pappso::OboPsiModTerm::m_firstParse

staticprivate

Definition at line 75 of file obopsimodterm.h.

Referenced by parseLine().

◆ m_firstParseUnimod

QRegularExpression pappso::OboPsiModTerm::m_firstParseUnimod

staticprivate

Definition at line 78 of file obopsimodterm.h.

Referenced by parseLine().

◆ m_formula

QString pappso::OboPsiModTerm::m_formula

Definition at line 63 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), operator=(), parseLine(), and pappso::ChemicalFormula::setOboPsiModTerm().

◆ m_isA

QStringList pappso::OboPsiModTerm::m_isA

Definition at line 69 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), isA(), operator=(), parseLine(), and pappso::ChemicalFormula::setOboPsiModTerm().

◆ m_isUnimod

bool pappso::OboPsiModTerm::m_isUnimod = false

private

Definition at line 83 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), isUnimod(), operator=(), parseLine(), and setAccession().

◆ m_massMono

double pappso::OboPsiModTerm::m_massMono

Definition at line 67 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), operator=(), and parseLine().

◆ m_name

QString pappso::OboPsiModTerm::m_name

Definition at line 58 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), pappso::AaModification::createInstance(), pappso::AaModification::createInstance(), pappso::AaModification::createInstanceC13N15LabelledAminoAcid(), pappso::OboTermForm::displayOboTerm(), pappso::MsFileAccessor::getOboPsiModTermFileFormat(), pappso::TimsMsRunReaderBase::getOboPsiModTermInstrumentModelName(), pappso::PwizMsRunReader::getOboPsiModTermNativeIDFormat(), operator=(), parseLine(), pappso::FilterOboPsiModTermName::setOboPsiModTerm(), and pappso::MzIdentMlWriter::writeCvParam().

◆ m_origin

QString pappso::OboPsiModTerm::m_origin

Definition at line 64 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), pappso::AaModification::createInstance(), pappso::OboTermForm::displayOboTerm(), operator=(), parseLine(), and pappso::ChemicalFormula::setOboPsiModTerm().

◆ m_parseDefinition

QRegularExpression pappso::OboPsiModTerm::m_parseDefinition

staticprivate

Definition at line 79 of file obopsimodterm.h.

Referenced by parseLine().

◆ m_psiModLabel

QString pappso::OboPsiModTerm::m_psiModLabel

Definition at line 60 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), clearTerm(), pappso::OboTermForm::displayOboTerm(), operator=(), parseLine(), and pappso::FilterOboPsiModTermLabel::setOboPsiModTerm().

◆ m_psiMsLabel

QString pappso::OboPsiModTerm::m_psiMsLabel

Definition at line 61 of file obopsimodterm.h.

Referenced by OboPsiModTerm(), operator=(), parseLine(), and pappso::FilterOboPsiModTermLabel::setOboPsiModTerm().

◆ OboPsiMod

friend pappso::OboPsiModTerm::OboPsiMod

private

Definition at line 35 of file obopsimodterm.h.

◆ OboPsiMs

friend pappso::OboPsiModTerm::OboPsiMs

private

Definition at line 36 of file obopsimodterm.h.

◆ OboUnimod

friend pappso::OboPsiModTerm::OboUnimod

private

Definition at line 37 of file obopsimodterm.h.

The documentation for this class was generated from the following files:

pappsomspp/core/obo/obopsimodterm.h
pappsomspp/core/obo/obopsimodterm.cpp

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OboPsiModTerm() [1/2]

◆ ~OboPsiModTerm()

◆ OboPsiModTerm() [2/2]

Member Function Documentation

◆ clearTerm()

◆ getAccession()

◆ isA()

◆ isUnimod()

◆ isValid()

◆ operator=()

◆ parseLine()

◆ setAccession()

Member Data Documentation

◆ m_accession

◆ m_definition

◆ m_diffFormula

◆ m_diffMono

◆ m_findExactPsiModLabel

◆ m_findRelatedPsiMsLabel

◆ m_firstParse

◆ m_firstParseUnimod

◆ m_formula

◆ m_isA

◆ m_isUnimod

◆ m_massMono

◆ m_name

◆ m_origin

◆ m_parseDefinition

◆ m_psiModLabel

◆ m_psiMsLabel

◆ OboPsiMod

◆ OboPsiMs

◆ OboUnimod